Hiii,
1. I have run the above command . And i got the name.frcmod file.Which I am
attaching here below.
How to interpret this file so that i get to know parameters are taken from
which file ?
2.I am attaching the pdf format of modified parameters file in this mail.
I don't see any specification of angle and dihedral angle category.
Can you guide me for the same.
How to look for them?
TIA!
On Mon, Mar 9, 2020 at 3:53 AM Kellon Belfon <kellonbelfon.gmail.com> wrote:
> 1. I think the order you have is correct. The parameters in your modified
> leaprc (leaprc.ff101) should overwrite any similar definition in the ff99SB
> leaprc, if it is loaded after the ff99SB leaprc. To double check if you
> have the right parameters you can use parmed.
>
> parmed topology_file
> writeFrcmod name.frcmod
>
> Then you can look at the name.frcmod file to see if it have the parameters
> you intend to use.
>
> 2. The warning is letting you know that you did not define enough
> parameters for an Improper dihedral. Which leads me to ask this question.
> Which section of the file, loaded by loadAmberParams do you have the
> definition for HW OW HW? Is it under IMPROPER or ANGLE? It should be under
> the ANGLE section.
>
> On Sun, Mar 8, 2020 at 1:59 PM ankita mehta <mehtaroadies.gmail.com>
> wrote:
>
> > Thanks for the reply .
> > I managed to correct the formatting.
> > Now, I am having following concerns.
> > 1. I have two files from which parameters can be loaded .
> > One is leaprc.ff99SB and other one is modified leaprc.ff101.
> > Now, how to be sure that amber parameters of modified parameters will be
> > loaded.
> > Is there any connection in what order i write them in tleap , that order
> > it reads the parameters.
> >
> > 2. I am having some warning after loading the both parameters files:
> > Improper torsion lines
> > : what to do to correct this warning?
> >
> > Thanks!
> >
> >
> >
> > On Fri, Mar 6, 2020 at 6:30 PM David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Fri, Mar 06, 2020, ankita mehta wrote:
> > >
> > > >I am just using the modified force field parameters .
> > > >But it is giving me syntax error.
> > > >Can anyone guide me for the same.
> > >
> > > Your "leaprc.ff100" is not a leaprc-like file that can be sourced from
> > > the command line in tleap. Instead, you need to use loadAmberParams to
> > > load in a file like this.
> > >
> > > The file format info at http://ambermd.org/FileFormats.php#frcmod
> > > indicates that these files are fixed format, with entries in particular
> > > columns. Your file is "free format", with just spaces between the
> > > fields. I'm not sure whether loadAmberParams will work on that or not.
> > > Note that the supporting information file you used has the data
> > > carefully laid out in particular columns.
> > >
> > > ....dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Kellon A. A. Belfon, Graduate Student
> Carlos Simmerling Laboratory
> The Laufer Center for Physical and Quantitative Biology
> The Department of Chemistry, Stony Brook University
> Stony Brook, New York 11794
> Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
> <kellon.belfon.stonybrook.edu>edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 09 2020 - 10:00:02 PDT
